The semi-final draw will be made on Sunday after the Newcastle v Cardiff Blues and Wasps v Gloucester games.
The match-up between the two British and Irish Lions fly-halves had been talked up before the game, and the two swapped penalties in the opening 10 minutes.
Jones was soon getting under the skin of Toulon's Australian talisman Williams, sparking a stand-off between the sides after pushing the centre into touch.
The rugby league international lost composure again with a high tackle on Regan King, but Jones could not convert.
Toulon hooker Phillip Fitzgerald burst through a ruck on the Scarlets' 22 with the line at his mercy, only to throw a certain scoring pass to Scarlets centre Jonathan Davies.
An Andy Fenby run allowed Jones to edge the visitors in front with a superb long-range penalty.
The Llanelli side's composed opening was spoiled, though, when wing Sean Lamont conceded a penalty at a ruck on his 22.
Toulon captain Matt Henjak reacted instantly by running the ball, quickly feeding wing Marienval who squeezed over in the corner past the despairing challenge of Rhys Priestland.
Wilkinson converted superbly from the sidelines and - despite missing the chance to extend the lead when a drop goal drifted wide - added two more penalties before the break as the Scarlets' discipline began to falter.
The Scarlets needed the first score in the second half, but conceded again two minutes after the break.
Stephen Jones finds the going tough against a formidable Toulon side
Young scrum-half Tavis Knoyle did well to gather a high kick on halfway, only to lose it on the floor.
Marienval received the turnover ball in midfield and grubber-kicked through Lamont's legs, the wing having the speed to regather and the composure to ground the ball over his head when brought down on his back a yard from the line.
Jones hauled the Scarlets back with two quick penalties as Toulon were warned for their negative play at the breakdown, although he missed with a more difficult third.
The visitors were troubling Toulon with some exciting attacking play, a fine Wilkinson tackle needed to deny Davies at the corner.
The attack continued, Ken Owens stopped on the line, and Marienval was sent to the sin bin for a deliberate knock-on.
The Scarlets could not take advantage of the extra man, though, and as Marienval was about to return the visitors were reduced to 14, Rob McCusker sin-binned for an off-the-ball shoulder charge.
The video referee denied Luke Rooney a try because of a knock-on following a controversial move in which Priestland's attempts to defend seemed to be interfered with by Sinzelle.
The Scarlets held out gamely until the closing 10 minutes when Toulon's replacement strength told, Joe van Niekerk ripping the visitors apart in midfield.
Delightful handling kept the momentum going, Rooney freeing Sinzelle for a try in the corner that Wilkinson, for once, could not convert.
Pierre Mignoni was now pulling the strings from scrum-half, directing an attack that saw Mati Kefu burst the line before the phenomenal Williams went over for the fourth try, Tom May missing the conversion.
Scarlets resistance was finally shattered as they sought the final whistle, Toulon denied another score by a forward pass.
Then, with the final play of the game, man-of-the-match Missoup crashed over from short range for a try, May missing the simple conversion.
The defeat further diminishes the Scarlets' slim hopes of Heineken Cup qualification for next season.
They are likely to finish as the bottom Welsh region in the Magners League, and their best hope of making the Heineken could be if the Blues win the Amlin.
Toulon coach Phillippe Saint Andre: "I'm very pleased, there was a good team spirit after I made a number of changes from last week, they showed a lot of commitment.
"We were penalised a lot early on, I don't understand why.
"But then we scored four tries and played very well."
Scarlets fly-half Stephen Jones: "We gave it our best shot and have to give a lot of credit to Toulon.
"They were very well drilled, played some great rugby, had very strong forwards, a great platform - and they used that possession wisely and efficiently, it was a tough night for us.
"It's a fantastic place to play, you love coming to places like this, it's always a challenge and a tough test.
"We are obviously disappointed with the result. We have a young squad and I'm sure that the guys will learn a lot from the experience, we have three massive league games left."
Toulon: Rooney, Marienval, May, Bill Williams, Sinzelle, Wilkinson, Henjak, Taumoepeau, Fitzgerald, Lea'aetoa, Suta, Lozada, Missoup, Sourice, Auelua. Replacements: Djoudi, Basteres, Ryan, Skeate, van Niekerk, Kefu, Mignoni, Beal.
Scarlets: Priestland, Lamont, King, J. Davies, Fenby, S. Jones, Knoyle, I. Thomas, Owens, Manu, Reed, Day, McCusker, Pugh, Lyons. Replacements: Phillips, John, R. Thomas, Welch, Turnbull, Roberts, Evans, Maule.
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